Data Visualization
Rachael E. Blake
January 13, 2022
Invertebrates: Percent Cover Data
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PDO phase plotted with mussel, fucus, and barnacle anomalies
Freshwater discharge plotted with mussel, fucus, and barnacle anomalies
Mytilus Anomaly with Air Temp
Fucus Anomaly with Air Temp
Barnacle Anomaly with Air Temp
Air Temperature plots
Air Temperature Anomalies with mussels, fucus, and barnacles
NMDS Plots
PDO
PDO Permanova Results
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## Call:
## vegan::adonis(formula = sp_percov ~ PDO_anul_mn, data = pdo_treats, permutations = 1000, method = "bray")
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## Permutation: free
## Number of permutations: 1000
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## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## PDO_anul_mn 1 0.13842 0.138416 3.4099 0.13969 0.01299 *
## Residuals 21 0.85244 0.040592 0.86031
## Total 22 0.99085 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Freshwater Discharge
Freshwater Discharge Permanova Results
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## Call:
## vegan::adonis(formula = sp_percov2 ~ mean_yearly_discharge_m3d1, data = fresh_treats, permutations = 1000, method = "bray")
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## Permutation: free
## Number of permutations: 1000
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## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## mean_yearly_discharge_m3d1 1 0.01886 0.018856 0.43699 0.0237 0.7982
## Residuals 18 0.77670 0.043150 0.9763
## Total 19 0.79556 1.0000Air Temperature
Air Temp Permanova Results
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## Call:
## vegan::adonis(formula = sp_percov3 ~ ATemp_yearMn, data = atemp_treats, permutations = 1000, method = "bray")
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## Permutation: free
## Number of permutations: 1000
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## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## ATemp_yearMn 1 0.10530 0.105297 2.497 0.10627 0.03297 *
## Residuals 21 0.88556 0.042169 0.89373
## Total 22 0.99085 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1All env. variables
All env. vars Permanova Results
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## Call:
## vegan::adonis(formula = sp_percov4 ~ ATemp_yearMn + mn_yr_discharge, data = all_treats, permutations = 1000, method = "bray")
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## Permutation: free
## Number of permutations: 1000
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## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## ATemp_yearMn 1 0.09312 0.093121 2.37670 0.11705 0.05095 .
## mn_yr_discharge 1 0.03636 0.036361 0.92803 0.04570 0.43556
## Residuals 17 0.66608 0.039181 0.83724
## Total 19 0.79556 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Biological NMDS
Hulls representing each Quadrat
Hulls representing each Year
Ordinations with taxa vectors
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## ***VECTORS
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## MDS1 MDS2 r2 Pr(>r)
## FUCUS_PERCOV_TOTAL 0.28514 -0.95849 0.6046 0.000999 ***
## BARNACLES 0.85840 0.51298 0.1465 0.000999 ***
## MYTILUS -0.99993 -0.01193 0.3527 0.000999 ***
## PTEROSIPHONIA -0.96072 -0.27753 0.4351 0.000999 ***
## BARNACLE_SPAT -0.28529 0.95844 0.0757 0.000999 ***
## FUCUS_SPORELINGS_PERCOV 0.14829 -0.98894 0.0419 0.006993 **
## LOTTIIDAE -0.64317 0.76572 0.2235 0.000999 ***
## L.SITKANA 0.78749 0.61633 0.0312 0.034965 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 1000
Ordinations with env. vectors
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## ***VECTORS
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## MDS1 MDS2 r2 Pr(>r)
## mn_yr_discharge -0.45663 -0.88966 0.0026 0.73027
## ATemp_yearMn -0.92954 0.36871 0.0287 0.02597 *
## Water_Temp_June -0.98194 -0.18917 0.0382 0.01099 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 1000
Permanova Results
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## Call:
## vegan::adonis(formula = sp_percov5 ~ ATemp_yearMn * mn_yr_discharge * Water_Temp_June, data = all_treats2, permutations = 1000, method = "bray")
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## Permutation: free
## Number of permutations: 1000
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## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model
## ATemp_yearMn 1 0.9871 0.9871 9.951
## mn_yr_discharge 1 3.1919 3.1919 32.178
## Water_Temp_June 1 0.3839 0.3839 3.871
## ATemp_yearMn:mn_yr_discharge 1 0.1628 0.1628 1.641
## ATemp_yearMn:Water_Temp_June 1 0.3082 0.3082 3.108
## mn_yr_discharge:Water_Temp_June 1 0.3586 0.3586 3.615
## ATemp_yearMn:mn_yr_discharge:Water_Temp_June 1 0.0775 0.0775 0.781
## Residuals 232 23.0129 0.0992
## Total 239 28.4830
## R2 Pr(>F)
## ATemp_yearMn 0.03465 0.000999 ***
## mn_yr_discharge 0.11206 0.000999 ***
## Water_Temp_June 0.01348 0.003996 **
## ATemp_yearMn:mn_yr_discharge 0.00572 0.161838
## ATemp_yearMn:Water_Temp_June 0.01082 0.018981 *
## mn_yr_discharge:Water_Temp_June 0.01259 0.009990 **
## ATemp_yearMn:mn_yr_discharge:Water_Temp_June 0.00272 0.555445
## Residuals 0.80795
## Total 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Correlations between env. variables
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
Correlations between other variables
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
###Looking at lagged June water temp
